Magnesium in PDB 5zqa: Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form

The structure of Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form, PDB code: 5zqa was solved by J.H.Jeong, Y.G.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.29 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.669, 74.582, 74.955, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 18.9

The binding sites of Magnesium atom in the Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form (pdb code 5zqa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form, PDB code: 5zqa:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.3 occ:1.00 O A:HOH532 2.0 22.9 1.0 O A:HOH479 2.1 27.7 1.0 O A:HOH406 2.1 23.2 1.0 O A:HOH484 2.1 23.8 1.0 OE1 A:GLU70 2.1 17.7 1.0 CD A:GLU70 3.1 15.8 1.0 OE2 A:GLU70 3.3 14.8 1.0 O A:HOH501 4.3 22.8 1.0 O A:HOH437 4.3 25.7 1.0 ND2 A:ASN74 4.3 21.2 1.0 OD1 A:ASN74 4.4 20.9 1.0 CG A:GLU70 4.4 11.9 1.0 CG A:ASN74 4.8 18.4 1.0 CB A:GLU70 4.9 10.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:0.4 occ:1.00 OE2 A:GLU187 1.9 13.7 1.0 O A:HOH405 2.0 12.6 1.0 ND1 A:HIS185 2.1 11.3 1.0 CD A:GLU187 2.8 11.2 1.0 CE1 A:HIS185 3.0 10.5 1.0 OE1 A:GLU187 3.0 10.3 1.0 CG A:HIS185 3.1 8.7 1.0 OD2 A:ASP73 3.3 16.9 1.0 CB A:HIS185 3.4 10.3 1.0 OD1 A:ASP73 3.7 21.7 1.0 O A:HOH554 3.8 20.8 1.0 CG A:ASP73 3.9 20.2 1.0 CA A:HIS185 3.9 9.3 1.0 CB A:LEU69 4.1 8.0 1.0 NE2 A:HIS185 4.1 11.3 1.0 CG A:GLU187 4.2 11.4 1.0 CD2 A:HIS185 4.2 10.5 1.0 CD2 A:LEU69 4.3 11.1 1.0 O A:LEU69 4.5 9.6 1.0 O A:THR184 4.5 9.8 1.0 CG A:LEU69 4.6 8.5 1.0 CD1 A:LEU69 4.8 12.3 1.0 C A:LEU69 4.8 9.2 1.0 C A:HIS185 4.9 9.7 1.0 CA A:LEU69 4.9 7.6 1.0 N A:HIS185 5.0 10.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Penicillin-Binding Protein D2 From Listeria Monocytogenes in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:33.7 occ:1.00 O A:HOH410 2.1 28.2 1.0 O A:HOH542 2.2 33.4 1.0 O A:HOH427 2.3 27.1 1.0 O A:ASP227 4.1 20.5 1.0 OD1 A:ASP250 4.3 18.6 1.0 OD2 A:ASP250 4.3 20.7 1.0 O A:GLU228 4.4 18.8 1.0 O A:HOH417 4.7 29.1 1.0 CG A:ASP250 4.7 18.2 1.0

J.H.Jeong, H.J.Cha, Y.G.Kim. Crystal Structures of Penicillin-Binding Protein D2 From Listeria Monocytogenes and Structural Basis For Antibiotic Specificity Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30082290
DOI: 10.1128/AAC.00796-18